IMAP-PART 09

Multi-Dimensional Data Visualization with integrated tools and Snakemake workflow

Fostering Reproducible Microbiome data visualization with Snakemake workflow

Microbiome Data Visualization

Do you know how to read .qza file?

## Reading and exploring Artifacts (.qza)
SVs <- read_qza(file = "data/feature_table.qza", tmp = "data/tmpdir", rm = TRUE)

SVs$data[1:4,1:4]

otu_table(q2_ps)[1:4,1:4]

## Reading metadata
read_q2metadata("data/sample_metadata.tsv")[1:5, 1:5]

read_tsv("data/sample_metadata.tsv", comment = "#q2:types", show_col_types = FALSE)[1:5, 1:5] %>% 
  rename(SampleID="#SampleID")

## Reading taxonomy
taxonomy<-read_qza("data/taxonomy.qza")
head(taxonomy$data)

## Parse tidy taxonomy only
taxonomy<-parse_taxonomy(taxonomy$data)
head(taxonomy)

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using MOTHUR and Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 and Snakemake workflows	In-progress
IMAP-PART 07	Processing Output from 16S-Based microbiome bioinformatics pipelines	In-progress
IMAP-PART 08	Exploratory Analysis of 16S-Based Microbiome Processed Data	In-progress
IMAP-PART 09	Visualization of Microbiome Profiles with Snakemake workflows	In-progress
IMAP-SUMMARY	Summary of snakemake workflows for microbiome data analysis	In-progress

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── README.md
├── Rplots.pdf
├── config
│   ├── config.yml
│   ├── pbs
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   ├── samples.tsv
│   ├── slurm
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature_table.qza
│   ├── features.csv
│   ├── metadata.csv
│   ├── metadata.tsv
│   ├── q2_demo_ps.rds
│   ├── q2_ps.rds
│   ├── sample_metadata.tsv
│   ├── shannon.csv
│   ├── shannon.qza
│   ├── taxonomy.csv
│   └── taxonomy.qza
├── figures
│   ├── heatmap.png
│   ├── heatmap.svg
│   ├── jitterplot.png
│   ├── jitterplot.svg
│   ├── lineplot.png
│   ├── lineplot.svg
│   ├── pcoa.png
│   ├── pcoa.svg
│   ├── venndiagram.png
│   └── venndiagram.svg
├── images
│   ├── bkgd.png
│   ├── coders.png
│   ├── ml.png
│   ├── smkreport
│   │   └── screenshot.png
│   └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── resources
│   ├── feature_table.qza
│   ├── rooted_tree.qza
│   ├── sample_metadata.tsv
│   ├── shannon_vector.qza
│   ├── tax.qza
│   ├── taxonomy.qza
│   └── unweighted_unifrac_pcoa.qza
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── environment.yml
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmap.rst
    │   ├── jitterplot.rst
    │   ├── lineplot.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoa.rst
    │   ├── scatter.rst
    │   ├── venndiagram.rst
    │   └── workflow.rst
    ├── rules
    │   ├── qiime2_viz.smk
    │   ├── render_index.smk
    │   ├── rmd_report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── common.R
        ├── convert_qiime2csv.R
        ├── heatmap.R
        ├── import_qiime2_data.R
        ├── jitterplot.R
        ├── lineplot.R
        ├── pcoa.R
        ├── qiime2R.R
        ├── qiime2_phyloseq_object.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        ├── tree.sh
        └── venndiagram.R

16 directories, 89 files

Unlocking working directory.
Building DAG of jobs...
Creating report...
Adding venndiagram.svg (0.17 MB).
Adding lineplot.svg (0.016 MB).
Adding jitterplot.svg (0.014 MB).
Adding pcoa.svg (0.014 MB).
Adding heatmap.svg (0.19 MB).
Loading script code for rule qiime2_phyloseq_object
Loading script code for rule import_qiime2_data
Loading script code for rule import_demo_qiime2_data
Loading script code for rule venn_diagram
Loading script code for rule convert_qiime2csv
Loading script code for rule line_point_plot
Loading script code for rule jitter_plot
Loading script code for rule pcoa_ordination
Loading script code for rule heatmap_plot
Downloading resources and rendering HTML.
Report created: report.html.
[0409/015936.115087:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0409/015936.117128:ERROR:file_io.cc(91)] ReadExactly: expected 8, observed 0
[0409/015936.119403:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0409/015940.083604:INFO:headless_shell.cc(653)] Written to file /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png.
Created 1 file(s):
    /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on April 09, 2023.
Github_Repo: https://github.com/tmbuza/imap-data-visualization.
Repo compiled and maintained by: Teresia Mrema-Buza.